Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

Gene expression profiles of MCF-7 cells treated with Si-Wu-Tang, estradiol and ferulic acid

ABSTRACT: Traditional Chinese medicines (TCM), usually composed of a mixture of components, may simultaneously target multiple genes/pathways and thus achieve superior efficacy for complex diseases such as cancer. To identify novel mechanisms of action and potential health benefits for a TCM formula Si-Wu-Tang (SWT) widely used for womenâs health, we obtained the DNA microarray expression profiles for SWT, its active component ferulic acid, and estradiol in human breast cancer cell line MCF-7 and analyzed the gene expression signatures associated with each treatment using the âConnectivity Mapâ (cMAP). This study indicates that DNA microarray profiling analysis and cMAP data mining provide a powerful approach to discover unknown mechanisms of actions and identify potential new health benefits for TCM. We profiled the gene expression of MCF-7 cell lines to SWT, its active component FA, as well as estradiol using Affymetrix human genome U133 plus 2.0 arrays. The data set includes profiles for 24 samples, divided into eight groups of treatment: 0.001% DMSO used as the vehicle control (C), 0.1 ÂµM estradiol (EM), FA at three concentrations (0.1, 1, and 10 ÂµM) (FL, FM and FH) and SWT at three concentrations (0.0256, 0.256, and 2.56 mg/ml) (SL, SM and SH). For each treatment group, 3 biological replicates were included, resulting in 24 (8 groups Ã 3 replicates/group) RNA samples.

ORGANISM(S): Homo sapiens

SUBMITTER: Leming Shi

PROVIDER: E-GEOD-23610 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Publications

Discovery of molecular mechanisms of traditional Chinese medicinal formula Si-Wu-Tang using gene expression microarray and connectivity map.

Wen Zhining Z Wang Zhijun Z Wang Steven S Ravula Ranadheer R Yang Lun L Xu Jun J Wang Charles C Zuo Zhong Z Chow Moses S S MS Shi Leming L Huang Ying Y

PloS one 20110328 3

To pursue a systematic approach to discovery of mechanisms of action of traditional Chinese medicine (TCM), we used microarrays, bioinformatics and the "Connectivity Map" (CMAP) to examine TCM-induced changes in gene expression. We demonstrated that this approach can be used to elucidate new molecular targets using a model TCM herbal formula Si-Wu-Tang (SWT) which is widely used for women's health. The human breast cancer MCF-7 cells treated with 0.1 µM estradiol or 2.56 mg/ml of SWT showed dram ...[more]

PMID: 21464939

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Project description:The long-term goal of our study is to understand the genetic and epigenetic mechanisms of breast cancer metastasis in human and to discover new possible genetic markers for use in clinical practice. We have used microarray technology (Human OneArray microarray, phylanxbiotech.com) to compare gene expression profiles of non-invasive MCF-7 and invasive MDA-MB-231 cells exposed to dioscin (DS), a steroidal saponin isolated from the roots of wild yam, (Dioscorea villosa). Initially the differential expression of genes (DEG) was identified that followed pathway enrichment analysis (PEA). Of the genes queried on OneArray, we identified 4641 DEG changed between MCF-7 and MDA-MB-231 cells (vehicle-treated) with cut-off log2 |fold change|â§ 1. Among these genes, 2439 genes are upregulated and 2002 genes are downregulated. DS exposure (2.30 ïM, 72 h) to these cells identified 801 (MCF-7) and 96 (MDA-MB-231) DEG that showed significant difference compared to untreated cells (p<0.05). Within these gene sets, DS is able to upregulate 395 genes and downregulate 406 genes in MCF-7 and upregulate 36 and downregulate 60 genes in MDA-MB-231 cells. Further comparison of DEG between MCF-7 and MDA-MB-231 cells exposed to DS identified 3626 DEG of which 1700 were upregulated and 1926 genes were down-regulated. From PEA, 12 canonical pathways were significantly altered between these two cell lines (MCF-7 and MDA-MB-231). However, no alteration in any of these pathways was noticed in MCF-7 cell, while in MDA-MB-231 cells only MAPK pathway showed significant alteration. When PEA comparison was made on DS exposed cells, it was observed that only 2 pathways were significantly affected. Further, to identify shared DEG, which are targeted by DS and overlapped in both MCF-7 and MDA-MB-231 cells, we performed intersection analysis (Venn diagram). We found that only 7 DEG are overlapped of which six are reported in the database. This study highlights the diverse gene networks and pathways through which DS exhibits its effect on breast cancer cells. Two condition experiment. Human breast cancer Cell line MCF-7 groups: Vehicle control and dioscin treated; Human breast cancer cell line MDA-MB-231 cell group; vehicle control and dioscin-treated. Biological replicates: MCF-7 control compared to MCF-7 dioscin treated; MDA-MB-231 control compated to MDA-MB-231 dioscin-treated; MCF-7 control compared to MDA-MB-231 control; MCF-7 dioscin treated compared to MDA-MB-231 dioscin-treated. duplicate array

Dataset Information

Gene expression profiles of MCF-7 cells treated with Si-Wu-Tang, estradiol and ferulic acid

Publications

Discovery of molecular mechanisms of traditional Chinese medicinal formula Si-Wu-Tang using gene expression microarray and connectivity map.

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